bulk_grep.pl

#!/usr/bin/env perl

# Searches all input files for queries listed in query list file.

# Usage:
# perl bulk_grep.pl [file listing queries, one per line] [file to grep]
# [another file to grep] [etc.]

# Prints to console. To print to file, use
# perl bulk_grep.pl [file listing queries, one per line] [file to grep]
# [another file to grep] [etc.] > [output file path]


use strict;
use warnings;


my $query_list_file = $ARGV[0];
my @files_to_grep = @ARGV[1..$#ARGV];


my $NEWLINE = "\n";


# verifies that input files exist and is not empty
if(!$query_list_file or !-e $query_list_file or -z $query_list_file)
{
	print STDERR "Error: query list file not provided, does not exist, or empty:\n\t"
		.$query_list_file."\nExiting.\n";
	die;
}
foreach my $file_to_grep(@files_to_grep)
{
	if(!$file_to_grep or !-e $file_to_grep or -z $file_to_grep)
	{
		print STDERR "Error: file to grep not provided, does not exist, or empty:\n\t"
			.$file_to_grep."\nExiting.\n";
		die;
	}
}

# read in query list and grep each query
open QUERY_LIST, "<$query_list_file" || die "Could not open $query_list_file to read; terminating =(\n";
while(<QUERY_LIST>) # for each line in the file
{
	chomp;
	if($_ =~ /\S/)
	{
		foreach my $file_to_grep(@files_to_grep)
		{
			print `grep "$_" $file_to_grep`;
		}
	}
}
close QUERY_LIST;


# August 17, 2021